Are you painting with the rubberized stuff to be more protective against scrapes? Regardless, it's not "correct" for the car so however you choose will make no difference really, just whatever you feel works best for your uses. The Plasti-dip type stuff can be peeled off eventually as long as you use several coats so it's thick enough, so if you use a similar product it won't be as big of a deal to remove later if you decide to.
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